I only have one input. The last posting's orig.jpg was 001.mgz, and
motioncor.jpg is orig.mgz. We usually run motioncor because it produces the
orig.mgz which has been conformed.
On Mon, Jun 3, 2013 at 2:41 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote:
> what does the 001.mgz look like? Do you have more than one input
> (otherwise you wouldn't need motion correction)? If so, you'll need to do
> this for each one
>
> On Mon, 3 Jun 2013, Erin Browning wrote:
>
> The orig.mgz is hyerintense (there's a screenshot of it in another post
>> now). The AFNI file is in float.
>> I ran:
>>
>> mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz -odt float
>> --out-scale 1.5 -ns 1
>>
>> and then I ran motioncor:
>>
>> recon-all -subjid freesurfer -motioncor
>>
>> Attached is what the scan looks like after each step; it's still coming
>> out
>> hyperintense like before. I'm concerned it will segment poorly again.
>>
>>
>>
>>
>>
>> On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>> wrote:
>> Hi Erin
>>
>> that can happen if you lose too much dynamic range when
>> "conforming". What does the orig.mgz look like? What voxel
>> format is the afni file in (uchar? float?) mri_convert has a -ns
>> 1 flag to turn off intensity scaling ("no scale"). If the brik
>> was in float you could use something like (from the mri dir)
>>
>> mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz
>> --out-scale <N> -ns
>>
>>
>> this will turn off auto scaling (-ns) then use the scale factor
>> you supply isntead (<N>), which you should estimate to bring
>> white matter intensities to around 110.
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Mon, 3 Jun 2013, Erin Browning wrote:
>>
>>
>> It seems like it getting darker messes up the
>> normalization later on; could
>> this be the case? Here's what it looks like in AFNI
>> (1029-afni.jpg), and
>> here's what it looks like after we run motioncor
>> (1029-orig.jpg).
>>
>>
>> On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve
>> <gr...@nmr.mgh.harvard.edu>
>> wrote:
>>
>> that will not change the intensities at all.
>> It is probably just
>> a display issue. Try changing the
>> brightness/contrast. The
>> artifact might cause problems later on, but
>> this is not an
>> issue I think
>> doug
>>
>> On 06/03/2013 02:20 PM, Erin Browning wrote:
>> We use:
>>
>> mri_convert N1029-anat+orig.BRIK
>> freesurfer/mri/orig/001.mgz
>>
>> where freesurfer is our freesurfer subject
>> folder.
>>
>>
>> On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve
>> <gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>
>> >>
>> wrote:
>>
>> what is your mri_convert command line?
>>
>> On 06/03/2013 02:11 PM, Erin Browning wrote:
>> > Hi everyone--
>> >
>> > We have a series of scans with an hyperintense
>> artifact
>> cutting
>> > through the temporal and frontal lobe. When we
>> run
>> mri_convert to
>> > convert from AFNI .BRIK files to .mgz fles,
>> the results
>> look
>> like the
>> > attached image.
>> >
>> > How can I correct for this? We tried
>> skullstripping in
>> AFNI first to
>> > remove some of the artifact, but that didn't
>> seem to help
>> very much.
>> >
>> > Thank you,
>> > Erin Browning
>> >
>> >
>> >
>> >
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>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>
>> >
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>> Bugs:
>>
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>
>>
>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> >
>> FileDrop:
>>
>> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2>
>>
>>
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>
>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**
>> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
>> Outgoing:
>>
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
>> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>>
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>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs:
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> FileDrop:
>> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2>
>>
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
>> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>>
>>
>>
>>
>>
>>
>>
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